TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv1885c/-:

update plot	correlation	link to info on gene
Rv1548c/PPE21	(cc=0.5453)	info on Rv1548c/PPE21
Rv2038c/-	(cc=0.4839)	info on Rv2038c/-
Rv3125c/PPE49	(cc=0.4827)	info on Rv3125c/PPE49
Rv2957/-	(cc=0.4605)	info on Rv2957/-
Rv1503c/-	(cc=0.4584)	info on Rv1503c/-
Rv1387/PPE20	(cc=0.4569)	info on Rv1387/PPE20
Rv1917c/PPE34	(cc=0.4569)	info on Rv1917c/PPE34
Rv2809/-	(cc=0.4557)	info on Rv2809/-
Rv1831/-	(cc=0.4544)	info on Rv1831/-
Rv0844c/narL	(cc=0.453)	info on Rv0844c/narL

Correlation of Rv1885c/- with Rv1548c/PPE21

Normalized LFCs for Rv1885c/-:
(description and provenance of datasets)

	Rv1885c/-	Rv1548c/PPE21
Fe_supp_jason_reseq	-0.204	0.44
low_pH_jason_reseq	-0.37	-0.494
NO_jason_reseq	-0.221	0.399
B6_jason_reseq	-0.127	-0.968
MHCII_jason_reseq	0.283	-1.76
Isoniazid02	-0.115	0.049
Rifampicin4	-0.574	0.439
Ethambutol3	0.129	-0.533
Meropenem3	0.028	-0.073
Vancomycin16	-0.732	0.0
Rv2680_day32	-0.112	-0.368
H37Rv_KO_MarP	0.109	0.268
hypoxia_3wks	0.08	0.243
hypoxia_6wks	-0.263	-0.177
glycerol	-0.252	0.143
cholesterol	-0.495	0.268
AJ	0.148	-0.467
Bibs02	-0.044	0.098
Bibs02c	-0.341	-0.517
BL6	0.592	1.274
BL6a	-0.125	0.753
BXD01	-0.012	0.409
BXD010	-0.281	0.83
BXD011	0.275	0.813
BXD03	0.223	0.677
BXD04	0.864	0.647
BXD05	0.115	1.082
BXD06	0.0	0.879
BXD07	0.346	1.053
BXD08	0.079	0.988
BXD09	0.09	1.13
CAST	0.01	0.933
CCcont	0.3	0.861
DS01	-0.546	0.043
DS02	-0.503	-0.588
DS04	-0.994	0.035
DS0c	-0.104	-1.042
GP01	-0.087	0.92
GP02	0.512	1.1
GP0c	0.172	1.231
NOD	0.308	1.565
NZO	0.24	0.072
PWK	0.054	0.139
H37Rv_KO_CtpC	0.418	1.99
H37Rv_KO_CtpD	0.298	1.77
H37Rv_KO_Rv1272	0.94	2.196
H37Rv_KO_SugABC	0.908	1.088
H37Rv_KO_MbtN	0.927	2.146
Trans05	1.173	2.226
macrophage_unactivated	-0.019	0.524
IL1	-0.839	0.492
Rapamycin	-0.298	0.193
Tcell	-0.098	0.401
GMCSF	0.121	1.159
IFNab	0.157	0.671
IFNg	-0.08	1.013
IFNg_GMCSF1	0.317	1.071
Rv1432_day32	0.297	0.209
Rv1565c_day32	-0.608	-0.22
secA2_input	-0.282	-0.512
delta_Rv3594	0.219	0.18
delta_Rv3717	-0.128	0.088
delta_Rv3811	0.355	-0.311
delta_Rv0954	-0.083	0.026
PonA1	-0.751	-0.325
EccD1_KO	0.474	-0.217
EspI_KO	-0.622	-0.031
PE35_KO	0.175	-0.128
PPE68_KO	-0.09	0.0
glycerol2	0.233	-0.028
lignocerate	0.304	0.564
oleate	-0.238	-0.362
phosphatidylcholine	-0.05	0.395
acetate	0.141	0.721
glucAc	0.311	0.657
Rv0950ko	0.19	0.229
Rv1096ko	-0.033	-0.57
Rv3684ko	-0.684	-0.789
delta_otsA_trehalose	-0.217	-0.25